org.openscience.cdk.io

Class MDLV3000Writer

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectWriter

org.openscience.cdk.io.MDLV3000Writer

All Implemented Interfaces:

Closeable, AutoCloseable, IChemObjectIO, IChemObjectWriter

public final class MDLV3000Writer
extends DefaultChemObjectWriter

Ctab V3000 format output. This writer provides output to the more modern (but less widely supported) V3000 format. Unlikely the V2000 format that is limited to 999 atoms or bonds V3000 can write arbitrarily large molecules. Beyond this the format removes some (but not all) ambiguities and simplifies output values with tagging (e.g 'CHG=-1' instead of '5'). Supported Features:

• Atom Block, non-query features
• Bond Block, non-query features
• Sgroup Block, partial support for all chemical Sgroups, complete support for: Abbreviations, MultipleGroup, SRUs, (Un)ordered Mixtures

The 3D block and enhanced stereochemistry is not currently supported.

Constructor Summary

Constructors

Constructor and Description
MDLV3000Writer() Default empty constructor.
MDLV3000Writer(OutputStream out) Create a new V3000 writer, output to the provided JDK output stream.
MDLV3000Writer(Writer writer) Create a new V3000 writer, output to the provided JDK writer.

Method Summary

Modifier and Type	Method and Description
boolean	accepts(Class<? extends IChemObject> c) Returns whether the given IChemObject can be read or written.
void	close() Closes this IChemObjectIO's resources.
void	customizeJob()
IResourceFormat	getFormat() Returns the IResourceFormat class for this IO class.
void	setWriter(OutputStream writer) Sets the OutputStream from which this ChemObjectWriter should write the contents.
void	setWriter(Writer writer) Sets the Writer from which this ChemObjectWriter should write the contents.
void	write(IChemObject object) Writes a molecule to the V3000 format.

Methods inherited from class org.openscience.cdk.io.ChemObjectIO

addChemObjectIOListener, addSetting, addSettings, fireIOSettingQuestion, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.openscience.cdk.io.IChemObjectIO

addChemObjectIOListener, addSetting, addSettings, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener

Constructor Detail

MDLV3000Writer

public MDLV3000Writer(Writer writer)

Create a new V3000 writer, output to the provided JDK writer.

Parameters:

writer - output location

MDLV3000Writer

public MDLV3000Writer(OutputStream out)
               throws CDKException

Create a new V3000 writer, output to the provided JDK output stream.

Parameters:

out - output location

Throws:

CDKException

MDLV3000Writer

public MDLV3000Writer()

Default empty constructor.

Method Detail

write

public void write(IChemObject object)
           throws CDKException

Writes a molecule to the V3000 format. Writes the content of "object" to output.

Parameters:

object - the object of which the content is outputted

Throws:

CDKException - state exception (e.g undef bonds), unsupported format feature, object not supported etc

setWriter

public void setWriter(Writer writer)
               throws CDKException

Sets the Writer from which this ChemObjectWriter should write the contents.

Throws:

CDKException

setWriter

public void setWriter(OutputStream writer)
               throws CDKException

Sets the OutputStream from which this ChemObjectWriter should write the contents.

Throws:

CDKException

getFormat

public IResourceFormat getFormat()

Returns the IResourceFormat class for this IO class.

accepts

public boolean accepts(Class<? extends IChemObject> c)

Returns whether the given IChemObject can be read or written.

Parameters:

c - IChemObject of which is tested if it can be handled.

Returns:

true, if the IChemObject can be handled.

close

public void close()
           throws IOException

Closes this IChemObjectIO's resources.

Throws:

IOException - when the wrapper IO class cannot be closed.

customizeJob

public void customizeJob()